Femtosecond laser inducing refractive index modification has provided a flexible avenue to three-dimensional photonic devices. Having polarization dependent guiding properties, femtosecond photowritten type II waveguide can be used as waveguide polarizer, but it experiences high loss for reserved polarization component. A new type of low loss waveguide polarizer fabricated in fused silica using femtosecond laser was reported. It consists of a type I waveguide in the middle and two type II nanograting traces on both sides. Based on the polarization dependent scattering properties of nanograting indued by femtosecond laser, the evanescent field of type I waveguide was modulated by the type II nanograting traces. Because the mode having a polarization perpendicular to the nanograting experiences a higher scattering loss compared with the mode having a polarization parellel to the nanograting, the latter was transmitted more efficiently. Firstly, polarization extinction ratio as a function of the separation between type I waveguide and type II nanograting trace was investigated. Using the best separation, polarization extinction ratio as a function of the length of type II nanograting trace was further investigated. Extinction ratio up to 15.91 dB between orthogonal polarizations have been realized with a separation of 6 μm and a type II nanograting trace length of 6 mm. Higher extinction ratio could be easily realized by increasing the length of type II nanograting traces or the amount of type II nanograting traces.